Conformational motions and ligand-binding underlying gating and regulation in IP3R channel

Here authors report cryo-EM structures of IP(3)R1 which provide atomic details of IP3, Ca2+ and ATP binding. Molecular motions of key domains and sidechains were found to regulate ligand binding and gating, which are validated by functional assays. Inositol-1,4,5-trisphosphate receptors (IP(3)Rs) are activated by IP3 and Ca2+ and their gating is regulated by various intracellular messengers that finely tune the channel activity. Here, using single particle cryo-EM analysis we determined 3D structures of the nanodisc-reconstituted IP(3)R1 channel in two ligand-bound states. These structures provide unprecedented details governing binding of IP3, Ca2+ and ATP, revealing conformational changes that couple ligand-binding to channel opening. Using a deep-learning approach and 3D variability analysis we extracted molecular motions of the key protein domains from cryo-EM density data. We find that IP3 binding relies upon intrinsic flexibility of the ARM2 domain in the tetrameric channel. Our results highlight a key role of dynamic side chains in regulating gating behavior of IP3R channels. This work represents a stepping-stone to developing mechanistic understanding of conformational pathways underlying ligand-binding, activation and regulation of the channel.

Automated summary

In this study, the cryo-EM structures of IP(3)R1 were determined, providing atomic details of IP3, Ca2+ and ATP binding. The authors identified the molecular motions of key domains and sidechains that regulate ligand binding and gating behavior of IP3R channels.